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  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
  • C12Q1/701—Specific hybridization probes
  • C12Q1/708—Specific hybridization probes for papilloma
• • C—CHEMISTRY; METALLURGY
  • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
  • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
  • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
  • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
  • C12Q1/6844—Nucleic acid amplification reactions
  • C12Q1/686—Polymerase chain reaction [PCR]

Definitions

• This invention relates to a method for the detection of specific DNA regions of human papilloma-virus (hereinafter referred to as HPV). This invention also relates to a detection kit which is to be used for this method.
• HPV human papilloma-virus
• HPV HPV
• M. Durst et al., Proc. Natl. Acad. Sci. USA, 80, 3812-3815, 1983 More than 50 types of HPV have been identified, and HPV 16 has been detected in 40-60% of the reported cases of this desease, HPV 18 in 10-20%, and other types of HPV, most often HPV 33, at a lower percentage.
• a culture system for such viruses has not yet been established for use as a detection method for HPV, and immunological detection is difficult, because the production of virus particles cannot be detected when the virus is in the form of viral DNA (i.e., not packed into particles).
• conventional methods for detection mainly involve detection of the viral gene itself.
• M. Dürst et al. found that some 60% of samples of tissue from cervical cancers contain HPV 16 or HPV 18 DNA. The sensitivity of the detection by Southern hybridization is at the level of 0.5-1.0 copy per cell. It has also been found that the DNA of HPV in tissues from cervical cancer is integrated into the human genome.
• the integrated DNA of HPV has, as a rule, a large number of deletions, and many cases have been found in which the only regions that are completely conserved of the original are the genes E6 and E7 (Schwarz et al., Nature, 314, 111-114, 1985).
• PCR polymerase chain reaction
• the PCR method can be used to amplify enzymatically and in a specific way only the target gene so that it is useful for the detection of the target gene, giving high specificity with only a small amount of sample.
• the enzyme used is, for example, heat-resistant enzyme Taq polymerase, and amplification is accomplished by a cycle of the step of denaturation of DNA at 94°C, followed by the step of annealing of primer DNA at 55°C and the step of enzymatic synthesis of complemen­tary DNA chains at 72°C, which cycle is repeated the desired number of times at these temperatures, resulting in the exponential amplification of the target gene.
• amplification is accomplished by a cycle of the step of denaturation of DNA at 94°C, followed by the step of annealing of primer DNA at 55°C and the step of enzymatic synthesis of complemen­tary DNA chains at 72°C, which cycle is repeated the desired number of times at these temperatures, resulting in the exponential amplification of the target gene.
• the target DNA is amplified about 100,000 times.
• This PCR method is the most useful for the detection of DNA of HPV with high sensitivity from a trace amount of sample.
• each type of HPV can be identified for type specifically, it is necessary to select a pair of primers for amplification which are type-specific, and to select probes for use in detection which are type-specific.
• the pair of primers selected and the selected probes must be suitable for the accurate detection of the presence of HPV in clinical specimens.
• the regions selected were L1 and E1-E2.
• the regions of HPV DNA other than E6 and E7 may have deletions when they are integrated into the human genome, and therefore, when regions L1 and E1-E2 are selected as the regions to be amplified during the detection of HPV, there is a risk of a negative result in cases in which HPV is actually present.
• the object of this invention is to provide a method for the detection of HPV DNA and to provide a kit which makes use of this method with which during the detection of the HPV DNA, the type of the virus is identified clearly, and the amplified region of HPV DNA is amplified with high sensitivity; also this method offers a standard for decisions about the malignancy of cervical tissue in terms of whether there is cervical cancer, a precancerous condition, or neither.
• this invention firstly relates to a method for the detection of HPV 16, HPV 18, HPV 33, or some combination of these viruses, which method makes use of amplification with the use of a pair of oligonucleotide primers consisting of at least one DNA region selected from part or all of the E6 or E7 regions of the HPV 16, HPV 18, and HPV 33 genomes.
• this invention relates to a detection kit for the detection by the use of the above mentioned method, which kit is characterized by containing a probe for the detection of amplified DNA, and also the primer pair for amplification of a specific DNA region or regions.
• steps taken include the selection of DNA region or regions specific to HPV 16, HPV 18, or HPV 33, within the limits of the DNA regions E6 and E7, which are ancient HPV genes which are present, without fail, present in human cells infected with HPV, and oligonucleotide primer DNA which is needed for the amplification of DNA of HPV by use of the PCR is synthesized, after which cellular DNA from human cells that are infected by HPV is isolated, and these regions are amplified by the PCR; it is necessary to select regions which are type-specific for the virus type and which moreover have high detection sensitivity.
• HPV 16 HPV 18, and HPV 33 were previously cloned, and their complete nucleotide sequences have been disclosed in Virology, 145, 181-185, 1985; Journal of Molecular Biology, 193, 599-608, 1987; and Journal of Virology, 58, 991-995, 1986.
• region I which is a specific region of DNA in HPV 16, HPV 18, and HPV 33
• region II which is a specific region of DNA in each of these three types of HPV
• oligonucleotide primer DNA which is a pair of primer DNAs, one of which has about 20 residues of the sense sequence of the amplified region from the 5′ terminus and the other of which has about 20 residues of the antisense sequence from the 3′ terminal.
• This pair of primers should be capable of annealing with the chosen DNA region mentioned before, and as one example of these, the primer DNA shown in Table 2 can be synthesized with use of a DNA synthesizer, and purified by HPLC.
• a genetic amplification kit which includes Taq polymerase and an automated genetic ampli­fication apparatus are commercially available from Perkin-­Elmer Cetus, and with their use, it is possible to use the pair of primers of this invention for the amplification reaction of specific DNA regions.
• agarose gel electrophoresis After the amplification, it is possible to use, for example, agarose gel electrophoresis, dot hybridization and the like for the detection of DNA of HPV.
• the different types of HPV are distinguished by the selection of probe DNA specific for a region of the DNA sequence of each type of HPV.
• probe DNA any probe DNA which satisfies the requirements given above can be used, and the probes listed in Table 3 give examples of such probes.
• the DNA of these probes can be synthesized and purified by the same methods mentioned before for primer DNA.
• the probe DNA can be detected with a high degree of sensitivity by labelling of the probe DNA.
• Any of the known methods for labelling may be employed, such as, for example, the labelling of the 5′ end of the probe DNA with 32P with the use of T4 polynucleotide kinase, in an isotopic labelling method, and also by non-isotopic labelling methods, such as the enzymatic labelling of probe DNA, fluorescence labell­ing, labelling with biotin-avidin, or by the introduction of sulfone groups into the probe DNA as in Chemprobe kit (Takara), plus the use of an antibody to these groups to recognize the probe.
• the template DNA sample containing a specific amount of HPV DNA can be amplified by PCR and detected by dot hybridization.
• the template DNA sample can be prepared by dilution of HPV DNA from cloned plasmids with genome DNA of normal cervical tissue.
• the pair of primers and the probes of this invention can be used in the detection of HPV DNA which is at the con­centration of 10 ⁇ 6, and it is possible with their use to detect with high sensitivity regions I and II in the DNA sequence, thus making possible detection of HPV 16, HPV 18, and HPV 33 with high sensitivity.
• HPV DNA was detected in samples of tissue from normal cervix at 2%, a lower rate than by the conventional methods, so that the method of this invention is particularly satisfactory in providing a standard for the detection of malignancy in cervical tissue.
• the pair of primers for amplification of the specific DNA regions of this HPV and the probes for the detection of the amplified DNA regions can be supplied in kit form, and it is possible with the use of the kit to detect readily human HPV 16, HPV 18, HPV 33, or some combination of these.
• the pair of primers which are needed for the amplification of regions I and II may be provided in the kit in a mixture, and if the sample being tested has HPV DNA in which either region I or region II DNA has undergone mutation, it is possible to amplify the HPV DNA, and when clinical tests are being done, it is possible to prevent false-negative results.
• the reagents for use with the kit may be in liquid form, and they can also be in lyophilized form.
• Cells of the human cervical carcinoma cell line SiHa contain 1-10 copies of HPV 16 DNA.
• HeLa cells contain 10-50 copies of HPV 18 DNA. These cells were cultured separately in 6 cm culture dishes each containing Dulbecco's modified Eagle medium (DMEM; Flow Laboratories) which contains 10% fetal bovine serum (FBS; Flow Laboratories), 100 units/ml streptomycin (Meiji Seika K.K.), and 100 units/ml penicillin (Banyu Pharmaceuticals Co., Ltd.). When the cell number reached about 106, the culture was stopped and the medium was removed.
• DMEM Dulbecco's modified Eagle medium
• FBS fetal bovine serum
• streptomycin Meiji Seika K.K.
• penicillin Banyu Pharmaceuticals Co., Ltd.
• the cells were washed with 5 ml of TE buffer (10 mM Tris-HCl, pH 8.0, and 1mM EDTA) containing 0.1M NaCl, and then 5 ml of 0.5% SDS was added to the dishes, which were then left for 20 minutes at room temperature. The cells were scraped from the dishes and collected in polystyrene tubes. To the tubes was added 5 ml of TE buffer containing protease K at a concentration of 100 ⁇ g/ml, and the tubes were kept at 70°C for 2 hr.
• TE buffer 10 mM Tris-HCl, pH 8.0, and 1mM EDTA
• the precipitate was rinsed with 80% ethanol, and dried. Then it was dissolved in 1 ml of sterilized water. About 100 ⁇ g of genome DNA was obtained.
• Specimens of cervical carcinoma tissue, condyloma acuminatum tissue, and normal cervical tissue from patients who underwent hysterectomy for uterine myeloma were obtained.
• the specimens weighing 100 mg each were cut into pieces with dissection scissors, and the same procedures as above were followed, with treatment with protease K and then with phenol and cloroform, giving about 100 ⁇ g of genome DNA.
• oligonucleotide probe DNA is needed.
• the primer DNA and probe DNA shown in Tables 2 and 3, respectively, were synthesized with a DNA synthesizer (Applied Biosystems), and after deprotection, the DNA was purified by ion-exchange HPLC on TSK gel in a DEAE-2SW column. It was then desalted on a Sep-Pak C18 column (Waters), and about 50 ⁇ g of each DNA was obtained.
• the tube was heated for 10 minutes at 94°C, and to the tube were added 10 ⁇ l of a solution provided in the Gene Amp Kit (Perkin-Elmer Cetus), which was 10x amplification buffer (100 mM Tris-HCl, pH 8.3, 500 mM KCl, 15 mM MgCl2, and 0.1% (w/v) gelatin), 16 ⁇ l of a 1.25 mM dNTP mixture (dATP, dGTP, dCTP, and dTTP), 1 ⁇ l of 20 ⁇ M p16-1 primer, 1 ⁇ l of 20 ⁇ M p16-2R primer, and 0.5 ⁇ l of 5 units/ ⁇ l Taq polymerase.
• the reaction mixture was made to 100 ⁇ l by the addition of sterilized water.
• the reaction was proceeded at 94°C for 1 minute for denaturation, at 55°C for 2 minutes for annealing of the primers, and at 72°C for 2 minutes for the synthetic reaction. This cycle was repeated for a total of 30 times. After the reaction, the mineral oil of the upper layer was removed. Then 10 ⁇ l of the reaction mixture was analyzed by gel electrophoresis on a mixture of 3% Nusieve GTG agarose and 1% Sea-kem agarose (FMC). The gel was stained with ethidium bromide and the DNA bands were examined. Amplified DNA was found.
• a band at the region of 140 base pairs (bp) was found with the DNA from SiHa cells and from specimens of cervical carcinoma from patients infected with HPV 16.
• DNA from HeLa cells, from specimens from patients with condyloma acuminatum, and from specimens from normal cervical tissue was not amplified, so the DNA of the p16-1 and p16-2R primers specifically amplified HPV 16 DNA.
• the primers p16-3 and p16-4R were used for the amplification of region II. Amplified DNA at the region of 89 bp was found in SiHa cells and in specimens from patients with cervical carcinoma who were infected with HPV 16.
• the reaction mixture obtained in (1-3) was heated at 94°C for 10 minutes and then rapidly cooled in an ice bath, so that the DNA was denatured. Then 1 ⁇ l of the reaction mixture was spotted on a nylon membrane (Schleicher & Shuell) and illuminated with ultraviolet light at 254 nm for 10 minutes to fix the DNA to the membrane.
• This membrane was kept in 10 ml of prehybridization buffer (5x Denhardt's solution, 5x SSC, 0.1% SDS with 100 ⁇ g/ml salmon sperm DNA) for 2 hours at 37°C for prehybridization.
• prehybridization buffer 5x Denhardt's solution, 5x SSC, 0.1% SDS with 100 ⁇ g/ml salmon sperm DNA
• probe DNA pB16-1 labelled at the 5′ end with 32P was added, and hybridization was carried out at 37°C for 2 hours.
• the membrane was washed twice for 10 minutes each time at room temperature in washing solution 1, which contained 0.1% SDS in 2x SSC, and next washed twice for 20 minutes each time at 55°C in washing 2, which contained 0.1% SDS in 0.2x SSC.
• the membrane was dried and then put into a cassette containing X-ray film (Fuji Film).
• the cassette was kept at -70°C for 3 hours to allow the film to be exposed for autoradiography.
• Hybridization was done in the same way with the use of the probe pB33-I and the pB18-I. No hybridization was found.
• the plasmid was the restriction fragment B from Pst I digestion which included regions E6 and E7 of HPV 16 DNA (1776 pb; Journal of Virology, 58, 979-982, 1986) inserted into the Pst I site of the vector pSV2neo (5.6 kb).
• the plasmid was designated p16PstIB.
• the length of the entire human genome DNA is 3 x 109 bp. So that there would be 10 copies of p16PstIB/­genome DNA, this plasmid was diluted in genome DNA obtained from normal cervical tissue by the methods of (1-1). In this step, 245 pg of p16PstIB was diluted with 10 ⁇ g of normal genome DNA. This mixture was diluted tenfolds with normal genome DNA, and model template DNA in which there were 10 to 10 ⁇ 6 copies of p16PstIB per genome DNA was prepared. Here, 1 ⁇ g of genome DNA with 10 ⁇ 6 copies of p16PstIB corre­sponded to about 10 ⁇ 6 pg of HPV DNA, which was roughly one molecule.
• DNA (7.9 kb) containing the E6 and E7 regions of HPV 18 was inserted into the Eco RI site of the Escherichia coli plasmid pBR322, giving a plasmid designated pHPV 18(EMBO J, 3, 1151-1157, 1984). Also, as template DNA, DNA (7.9 kb) containing the E6 and E7 regions of HPV 33 was inserted into the Bgl II site of the E. coli plasmid plink322, giving a plasmid designated pHPV33 (J. Virol., 58, 991-995, 1986).
• DNA (7.9 kb) containing the E6 and E7 regions of HPV 16 was inserted into the Eco RI site of the E. coli plasmid mentioned above, pBR322, giving plasmid pHPV16 (Proc. Natl. Acad. Sci. USA, 80, 3812-3815, 1983).
• Each of these template DNAs was used 1 ng and with 1 ⁇ g of genome DNA prepared from SiHa cells or HeLa cells by the methods of (1-1).
• pHPV33 When amplification was done with p33-1 and p33-2R as the primers, only pHPV33 showed a hybridization spot with probe pB33-I. This showed that when primer DNA for the corresponding type of the virus was used, the DNA of region I was specifically amplified, and it was possible to detect it with the appropriate probe DNA.
• the different template DNAs were amplified with the use of a reaction system that contained as the primers either p18-3 and p18-4R or else p33-3 and p33-4R, which were obtained by the methods of (1-2); as the probe DNAs pB18-II and pB33-II, obtained by the methods of (1-2), were used to detect region II of HPV 18 and HPV 33.
• region II was amplified, and it was possible to detect it with the appropriate probe DNA.
• the various template DNA plasmids were diluted with genome DNA obtained from healthy cervical tissue, and the appropriate pairs of primers and the appropriate probe were used for ampli­fication and detection.
• the results obtained above show that the virus types HPV 16, HPV 18, and HPV 33 can be efficiently identified by the use of regions I and II of HPV, and that detection at an extremely sensitive level is possible when pairs of primers and the probe used correspond to the HPV 16, HPV 18, and HPV 33 being tested for.
• a kit was prepared for the amplification and detection of HPV 16, HPV 18, and HPV 33 in samples.
• pB16-I, pB16-II, pB18-I, pB18-II, pB33-I, and pB33-II were dissolved separately in TE buffer, at the concentration of 2 ⁇ g in 20 ⁇ l, and these were named the HPV 16-I probe solution (component D), HPV 16-II probe solution (component E), HPV 18-I probe solution (component F), HPV 18-II probe solution (component G), HPV 33-I probe solution (component H), and HPV 33-II probe solution (component I).
• Components A, D, F, and H were provided together in an amplification and detection kit I for HPV; components B, E, G, and I were provided together in an amplification and detection kit II for HPV; and components C, D, E, F, G, H, and I were provided together in an amplification and detection kit III for HPV (Table 4).
• genome DNA was obtained from about 100 mg of tissue from 43 patients who underwent surgery for cervical carcinoma and from about 10 mg of tissue obtained during biopsy of 27 patients with precancerous tissue. Of these two pooled samples, about 100 ⁇ g and about 10 ⁇ g of genome DNA were obtained, respectively.
• HPV DNA could be detected in 36 specimens (84%).
• Table 5 Detection of HPV DNA in specimens of cervical carcinoma HPV 16 HPV 18 HPV 33 Overall 33/43 12/43 6/43 36/43 (77%) (28%) (14%) (84%)
• HPV DNA was detected in 5 of the 8 patients in CINI, in 7 of the 9 patients in CINII, and in 7 of the 10 patients in CINIII, so detection of HPV DNA was possible in all stages from CINI to CINIII.
• this invention provides a method for the detection with high sensitivity of HPV DNA, especially by the use of the PCR, in which regions I and II are identified, and by which method the HPV genome in cancerous tissue and precancerous tissue can be detected with high sensitivity; this invention also provides a kit which makes use of this method.

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